Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
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Genome-wide analysis of subependymomas shows underlying chromosomal copy number changes involving chromosomes 6, 7, 8 and 14 in a proportion of cases.
PMID 18397339 · PMC2659379 · Brain pathology (Zurich, Switzerland) · 2008 · 8 claims · 2 setups
Whole-genome aCGH reveals chromosomal copy number abnormalities in 5 of 12 (42%) subependymoma cases
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Has reproduction · 30
SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue.
PMID 32746857 · PMC7397585 · BMC plant biology · 2020 · 7 claims · 5 setups
Short-term heat stress strongly and specifically activates Hsps, Hsfs, FKBPs, calcium signaling, glutathione S-transferase, photosynthesis, and phytohormone signaling genes.
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Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.
PMID 17565693 · PMC1920519 · BMC genomics · 2007 · 8 claims · 4 setups
42 different CNVs were detected in 27 phenotypically normal individuals using 1 Mb resolution BAC array-CGH
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Human and mouse oligonucleotide-based array CGH.
PMID 16361265 · PMC1316119 · Nucleic acids research · 2005 · 8 claims · 8 setups
Oligo array CGH detects single copy gains, multi-copy amplifications, and homozygous/heterozygous deletions as small as 100 kb
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Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans.
PMID 16478714 · PMC1368655 · Nucleic acids research · 2006 · 7 claims · 6 setups
SNP-MaP allele frequency estimates from pooled DNA on the 100K microarray set correlate strongly with allele frequencies from individual genotyping
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Pooled DNA genotyping on Affymetrix SNP genotyping arrays.
PMID 16480507 · PMC1382214 · BMC genomics · 2006 · 7 claims · 4 setups
Pooled genotyping on Affymetrix 10K arrays estimates allele frequency differences between pools with accuracy comparable to lower-throughput pooling platforms.
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Has reproduction · 83
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.
PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups
MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.
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Has reproduction · 61
TEMP: a computational method for analyzing transposable element polymorphism in populations.
PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups
TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.
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Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.
PMID 20003400 · PMC2806376 · BMC genetics · 2009 · 7 claims · 4 setups
Pooled genotyping on the Affymetrix 500k platform using PPC yields highly accurate allele frequency estimates (correlation 0.988) comparable to or better than the 10k/100k platforms.
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MLGA--a rapid and cost-efficient assay for gene copy-number analysis.
PMID 17823203 · PMC2034490 · Nucleic acids research · 2007 · 8 claims · 4 setups
MLGA is a novel selector-based technique using multiplex ligation-dependent circularization of genomic DNA fragments for copy-number analysis
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Allelotyping of pooled DNA with 250 K SNP microarrays.
PMID 17367522 · PMC1839100 · BMC genomics · 2007 · 8 claims · 5 setups
The polynomial based probe specific correction (PPC) algorithm is the most accurate method for estimating allele frequency from pooled DNA.
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Has reproduction · 86
Assessing Bos taurus introgression in the UOA Bos indicus assembly.
PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups
Aligning divergent (cross-subspecies) sequence data detects substantially more SNVs than aligning to a same-subspecies reference, indicating reference/assembly bias in variant calling.
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PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.
PMID 16199750 · PMC1240117 · Nucleic acids research · 2005 · 7 claims · 6 setups
The PPC algorithm, which applies a probe-pair-specific second-degree polynomial correction, increases the accuracy of allele frequency estimates from pooled DNA compared with previously described algorithms
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A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.
PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups
SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays
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Has reproduction · 75
Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.
PMID 35983322 · PMC9378778 · Frontiers in microbiology · 2022 · 6 claims · 7 setups
RPL29 (60S ribosomal protein L29) is highly/consistently expressed across all COVID-19 infected groups regardless of severity, suggesting it as a novel host therapeutic target for mRNA-based nanomedicines.
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Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.
PMID 18842124 · PMC2569949 · BMC genomics · 2008 · 7 claims · 7 setups
GS-FLX pyrosequencing of pooled amplicons detects sequence variants with high specificity (99.95%) and no false negatives at ≥30× coverage
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Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.
PMID 15983137 · PMC1160521 · Nucleic acids research · 2005 · 8 claims · 4 setups
A codon usage similarity statistic (ε, based on squared/absolute differences of codon frequencies with an optimized amino acid usage factor) was developed to compare ORFs against a set of 80 reference genomes.
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Has reproduction · 78
annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.
PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups
annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.
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Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.
PMID 19055809 · PMC2657802 · BMC bioinformatics · 2008 · 7 claims · 5 setups
QC processes for identifying and removing low-quality spectra are often overlooked in proteomic profiling studies
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Has reproduction · 69
A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.
PMID 23496952 · PMC3655071 · BMC genomics · 2013 · 8 claims · 8 setups
Representative de novo transcriptome assemblies are generated with as few as ~20 million reads for single-tissue samples and ~30 million reads for whole animals at the mRNA-coverage level.